Hi Rosalia
once you have imported the data for a subject with -i , you
shouldn't specify it for subsequent analyses
cheers
Bruce
On Fri, 19 Oct 2018, Rosalia Dacosta
Aguayo wrote:
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Dear FreeSurfer team,
I am trying to run recon -all -autoreco
esurfer-boun...@nmr.mgh.harvard.edu] *Im Auftrag von *Rosalia Dacosta
> Aguayo
> *Gesendet:* Freitag, 19. Oktober 2018 14:40
> *An:* Freesurfer support list
> *Betreff:* Re: [Freesurfer] Problems to run -autorecon2
>
>
>
> *External Email - Use Caution*
>
Gesendet: Freitag, 19. Oktober 2018 14:40
An: Freesurfer support list
Betreff: Re: [Freesurfer] Problems to run -autorecon2
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Dear Falk,
Thank you very much.
Once last question: what would happen if I did run -autorecon1 without the
flags: -qcache -openmp 8
> Aguayo
> *Gesendet:* Freitag, 19. Oktober 2018 14:10
> *An:* Freesurfer support list
> *Betreff:* Re: [Freesurfer] Problems to run -autorecon2
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>
> *External Email - Use Caution*
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> Dear Falk,
>
>
>
> Thank you very much for your email
Von: freesurfer-boun...@nmr.mgh.harvard.edu
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] Im Auftrag von Rosalia Dacosta
Aguayo
Gesendet: Freitag, 19. Oktober 2018 14:10
An: Freesurfer support list
Betreff: Re: [Freesurfer] Problems to run -autorecon2
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Dear Falk,
Thank you very much for your email and explanation. It is working now.
I wonder how I could set the smoothing for autorecon3 as to run recon -all
-all I had the options: -qcache -openmp 8
Kind regards,
Rosalia
On Fri, Oct 19, 2018 at 2:06
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Dear Rosalina,
you should run recon-all -sd ~/Desktop/MS_STUDY/subjects -s 001 -autorecon2 and
everything will run nicely. You should not include the -i flag again if you
want to continue processing your data, as this flag tells FreeSurfer to create
